Homeodomain transcription factor T/EBP (thyroid-specific enhancer-binding protein), also called thyroid transcription factor 1 (TTF1) or NKX2.1, plays a role in regulating expression of thyroid and lung-specific genes such as those encoding thyroid peroxidase, thyroglobulin, and TSH receptor, and surfactant proteins A, B, and C, and Clara cell secretory protein, respectively. T/EBP is also essential for genesis of the thyroid, lung, and ventral forebrain, which was unequivocally demonstrated by the production of T/ebp-null mouse that is missing the thyroid and pituitary, and has severe defects in the lung and hypothalamus. Thus, T/EBP appears to be a master regulatory gene involved in the genesis of these organs by either directly or indirectly activating or suppressing downstream target genes. In order to understand the role of T/EBP during development and in the homeostasis of the thyroid and lung, a conditional knockout mouse line that deletes T/EBP expression only in the thyroid or lung has been being developed. Thyroids from embryos and adults at various ages with and without T/EBP deletion are examined by histopathological and immunohistochemical analyses using several antibodies including those against T/EBP and thyroglobulin, degree of T/EBP gene deletion by southern blotting, T/EBP levels by Northern and Western blotting, and biochemical analysis of TSH levels in serum. Three dimensional thyroid primary culture system in combination with recombinant adenovirus expressing Cre recombinase is applied to study the effect of T/EBP deletion on thyroid differentiation and to understand a possible role for T/EBP in thyroid differentiation. FACS analysis of thyroid cells demonstrated that T/EBP may be involved in maintaining a population of cells that have stem-cell like activities. Based on the hypothesis that mice with deleted T/EBP may be susceptible to chemical carcinogens, carcinogenesis studies are in progress. Identifying genes that are regulated by T/EBP and are involved in thyroid and lung organogenesis is another focus of our current research. To this end, thyroids or lungs were collected from T/ebp-null mouse and wild-type littermate embryos. Laser capture microdissection (LCM) was employed to isolate as tiny tissue as the thyroid primordium. Total RNAs prepared from LCM microdissected thyroid primordia or lungs were subjected to DNA microarrays. Several candidate genes were obtained that appear to be differentially expressed in the thyroid primodium or lung between T/ebp-null and wild-type mouse embryos. RT-PCR and in situ hybridization were used to confirm their differential expressions in embryonic thyroid primordium or lung. Clones that showed differential patterns of expression have been further subjected to molecular biological analysis such as promoter analysis of the genes.